Could you try and reproduce this issue with 1.8.4? The solution to ZF-7002 might have fixed this.

Posted by Martin Adler (madler) on 2009-06-26T02:38:00.000+0000

Now I have tested this issue against Zend Framework 1.8.4 Release (r16258).
It still throws both warnings related to the FrontController.php
as explained in the description, but the module bootstrap will be loaded without any warnings now.

Posted by Miroslav Kubelik (koubel) on 2009-06-27T15:29:31.000+0000

I also test it with ZF 1.8.4 (r16258) in real app and I think that everything is OK, no warnings for Module/Bootstrap.php and no for FrontController.php.
But there is one problem I think.

At all events, ZF 7002 fixed the Module/Bootstrap.php warnings.

FrontController.php warnings are gone because the front controller resource plugin is initialized in the constructor of
Zend_Application_Bootstrap_Bootstrap, this is parent for main boostraps in most situations.

But in situation, when the front controller plugin is initialized only from module bootstrap via code from Zend_Application_Module_Bootstrap
constructor: